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Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types

DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their...

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Autores principales: Yan, Haidan, Zhang, Dongwei, Liu, Hongbo, Wei, Yanjun, Lv, Jie, Wang, Fang, Zhang, Chunlong, Wu, Qiong, Su, Jianzhong, Zhang, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325317/
https://www.ncbi.nlm.nih.gov/pubmed/25673498
http://dx.doi.org/10.1038/srep08410
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author Yan, Haidan
Zhang, Dongwei
Liu, Hongbo
Wei, Yanjun
Lv, Jie
Wang, Fang
Zhang, Chunlong
Wu, Qiong
Su, Jianzhong
Zhang, Yan
author_facet Yan, Haidan
Zhang, Dongwei
Liu, Hongbo
Wei, Yanjun
Lv, Jie
Wang, Fang
Zhang, Chunlong
Wu, Qiong
Su, Jianzhong
Zhang, Yan
author_sort Yan, Haidan
collection PubMed
description DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their relationships among different genomic regions in human embryonic stem cells (H1), H1-derived neuronal progenitor cultured cells (NPC), and foetal fibroblasts (IMR90) using the Random forests classifier. Histone modifications achieved high accuracy in modelling DNA methylation patterns on a genome scale in the three cell types. The inclusion of sequence features helped improve accuracy only in non-promoter regions of IMR90. Furthermore, the top six feature combinations obtained by mean decrease Gini were important indicators of different DNA methylation patterns, suggesting that H3K4me2 and H3K4me3 are important indicators that are independent of genomic regions and cell types. H3K9me3 was IMR90-specific and exhibited a genomic region-specific correlation with DNA methylation. Variations of essential chromatin modification signals may effectively discriminate changes of DNA methylation between H1 and IMR90. Genes with different co-variations of epigenetic marks exhibited genomic region-specific biological relevance. This study provides an integrated strategy to identify systematically essential epigenetic and genetic elements of genomic region-specific and cell type-specific DNA methylation patterns.
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spelling pubmed-43253172015-02-20 Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types Yan, Haidan Zhang, Dongwei Liu, Hongbo Wei, Yanjun Lv, Jie Wang, Fang Zhang, Chunlong Wu, Qiong Su, Jianzhong Zhang, Yan Sci Rep Article DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their relationships among different genomic regions in human embryonic stem cells (H1), H1-derived neuronal progenitor cultured cells (NPC), and foetal fibroblasts (IMR90) using the Random forests classifier. Histone modifications achieved high accuracy in modelling DNA methylation patterns on a genome scale in the three cell types. The inclusion of sequence features helped improve accuracy only in non-promoter regions of IMR90. Furthermore, the top six feature combinations obtained by mean decrease Gini were important indicators of different DNA methylation patterns, suggesting that H3K4me2 and H3K4me3 are important indicators that are independent of genomic regions and cell types. H3K9me3 was IMR90-specific and exhibited a genomic region-specific correlation with DNA methylation. Variations of essential chromatin modification signals may effectively discriminate changes of DNA methylation between H1 and IMR90. Genes with different co-variations of epigenetic marks exhibited genomic region-specific biological relevance. This study provides an integrated strategy to identify systematically essential epigenetic and genetic elements of genomic region-specific and cell type-specific DNA methylation patterns. Nature Publishing Group 2015-02-12 /pmc/articles/PMC4325317/ /pubmed/25673498 http://dx.doi.org/10.1038/srep08410 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Yan, Haidan
Zhang, Dongwei
Liu, Hongbo
Wei, Yanjun
Lv, Jie
Wang, Fang
Zhang, Chunlong
Wu, Qiong
Su, Jianzhong
Zhang, Yan
Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title_full Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title_fullStr Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title_full_unstemmed Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title_short Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types
title_sort chromatin modifications and genomic contexts linked to dynamic dna methylation patterns across human cell types
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325317/
https://www.ncbi.nlm.nih.gov/pubmed/25673498
http://dx.doi.org/10.1038/srep08410
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